Multi-scale modeling of gas transport through channels in living cells

描述（由申请人提供）：气体跨细胞膜运输是最基本的生理过程之一，o2用于氧化代谢，CO2用于酸碱平衡，NH3用于废物处理。二氧化碳滞留和高氨血症是引起重大公共卫生关切的疾病的关键组成部分。传统的教条认为，所有的气体都是通过膜脂扩散穿过所有的细胞膜的。然而，一些膜是不透气的，需要蛋白质“气体通道”，如水通道蛋白AQP1（大量存在于红细胞中）和AQP5（大量存在于气道上皮中）来传导二氧化碳和NH3等气体。这些气体通过aqp的运动导致通道周围微域的pH值紊乱，我们可以使用pH微电极测量。然而，人们对气体传导的机制了解甚少。分子动力学模拟，电极接触模型球形细胞（爪蟾卵母细胞）表面下的pH值（pH值）的测量，以及解决这些pH值变化的数学模型，为CO2和NH3通过通道的运动提供了第一个见解。然而，对这种跨细胞膜运动的基本理解需要更先进的多尺度数学模型（微观、介观、亚宏观和宏观），以阐明正常和病理状态下气体渗透的机制。pi（博士）。Boron， Somersalo和Tajkhorshid)建议将最先进的分子动力学模拟和计算建模与新颖的实验研究相结合，以开发一个预测各种气体通过不同蛋白质组成的不同细胞膜渗透的数学模型，该模型基于在一系列空间和时间尺度上的互补方法的数据整合。我们将在Aim 1中运行NH3和CO2通过野生型、突变型、化学修饰型和金属结合型水通道蛋白的分子动力学模拟，以预测单通道渗透率（微观尺度），这将为Aim 2中的建模和Aim 3中的细胞生理学提供信息。在Aim 2中，我们将创建新的计算模型，通过脂质双分子层（介观尺度）、pHS电极下（亚宏观尺度）和整个细胞（宏观尺度）中的单个和多个水通道蛋白进行气体输送。最后，在Aims 3中，根据Aims 1和Aims 2，我们将使用电生理和光学方法验证卵母细胞的模拟和模型。

DESCRIPTION (provided by applicant): The transport of gases across cell membranes is one of the most fundamental of physiological processes-O2 for oxidative metabolism, CO2 for acid-base balance, and NH3 for waste disposal. CO2 retention and hyperammonemia are key components of diseases that are major public health concerns. The traditional dogma had been that all gases cross all cell membranes by diffusing through membrane lipid. However, some membranes are gas impermeable and require protein 'gas channels' such as the aquaporins AQP1 (abundant in red blood cells) and AQP5 (abundant in airway epithelia) to conduct gases such as CO2 and NH3. Movement of these gases through AQPs results in a disturbance of pH in microdomains around the channels that we can measure using a pH microelectrode. However, the mechanism of gas conduction is poorly understood. Molecular dynamic simulations, measurements of the pH beneath an electrode touching the surface (pHS) of a model spherical cell (Xenopus oocytes), as well as a mathematical model addressing these pHS changes have provided the first insights into CO2 and NH3 movement through channels. However, a fundamental understanding of such movements across cell membranes requires more advanced multi-scale mathematical models (microscopic, mesoscopic, sub-macroscopic and macroscopic) in order to elucidate mechanisms of gas permeation in normal and pathological states. The PIs (Drs. Boron, Somersalo, and Tajkhorshid) propose to combine state-of-the-art molecular dynamic simulations and computational modeling with novel experimental studies to develop a predictive mathematical model for permeation of various gases across diverse cell membranes of different protein composition, based on integration of data from complementary methodologies across a range of spatial and temporal scales. We will run molecular dynamic simulations of NH3 and CO2 passage through wild-type, mutant, chemically modified, and metal-bound aquaporins in Aim 1 to predict single channel permeabilities (microscopic scale) that will inform the modeling in Aim 2 and cell physiology in Aim 3. In Aim 2, we will create new computational models of gas transport through single and multiple aquaporins in a lipid bilayer (mesoscopic scale), beneath the pHS electrode (sub-macroscopic scale) and in the whole cell (macroscopic scale). Finally in Aim 3, informed by Aims 1 and 2, we will validate the simulations and models in oocytes using electrophysiological and optical methods.